Contacts of the strand formed by residues 18 - 25 (chain G) in PDB entry 6I53
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 18 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLY 4.7 2.7 - - - +
9G GLY* 4.0 38.8 - - - +
10G GLY 5.6 0.9 - - - -
11G LEU 5.1 4.5 - - - +
12G VAL* 4.6 18.2 - - + -
17G SER* 1.3 78.6 - - - +
19G ARG* 1.3 66.3 + - - +
20G VAL* 4.4 4.0 - - + -
81G GLN* 3.4 7.8 + - - -
82G LEU* 2.8 60.3 + - + +
85G LEU* 4.1 4.9 - - + -
119G VAL* 3.9 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLY* 3.4 18.2 - - - +
18G LEU* 1.3 80.8 - - - +
20G VAL* 1.3 68.1 + - - +
21G SER* 4.0 4.8 + - - +
70G SER* 3.6 10.7 + - - -
79G ASP* 2.7 42.5 + - + +
80G LEU 3.9 6.5 - - - +
81G GLN* 3.0 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLU* 5.6 0.2 - - - +
7G SER 3.3 17.0 - - - +
8G GLY* 3.9 10.3 - - - -
9G GLY 4.5 1.3 - - - +
18G LEU* 4.4 6.1 - - + -
19G ARG* 1.3 76.5 - - - +
21G SER* 1.3 58.9 + - - +
36G TRP* 3.6 32.0 - - + -
79G ASP* 3.6 0.5 - - - -
80G LEU* 2.9 33.9 + - + +
82G LEU* 3.7 33.2 - - + -
93G TYR* 4.5 6.7 - - + -
117G THR* 4.7 11.7 - - + +
119G VAL* 4.4 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLU* 3.6 2.4 - - - +
7G SER* 3.1 43.4 + - - +
19G ARG* 4.0 6.1 + - - -
20G VAL* 1.3 74.9 - - - +
22G CYS* 1.3 76.6 + - - +
23G ALA* 4.5 1.7 + - - +
36G TRP* 3.6 7.0 - - - -
77G SER* 4.9 4.2 - - - -
78G VAL 3.6 5.6 + - - -
79G ASP* 3.0 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LEU* 4.3 13.0 - - - -
5G GLN 3.5 12.8 - - - +
6G GLU* 4.2 4.9 - - + +
21G SER* 1.3 84.1 + - - +
23G ALA* 1.3 65.2 + - - +
34G MET* 4.6 1.9 - - - +
36G TRP* 3.6 11.9 - - + -
77G SER* 3.3 5.1 - - - -
78G VAL* 3.0 32.1 + - + +
95G CYS* 2.0 49.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLN 4.0 0.2 - - - +
4G LEU* 3.7 4.0 - - - -
5G GLN* 2.9 41.4 + - + +
6G GLU 5.6 0.2 - - - -
21G SER* 4.5 2.3 + - - +
22G CYS* 1.3 77.3 - - - +
24G ALA* 1.3 61.4 + - - +
75G LYS 5.6 2.5 - - - +
76G ASN 5.0 0.2 - - - +
77G SER* 4.1 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLN 3.8 4.7 - - - -
4G LEU* 3.7 10.3 - - + -
23G ALA* 1.3 77.4 - - - +
25G SER* 1.3 66.0 + - - +
29G PHE* 3.6 34.5 - - + -
34G MET* 4.5 4.9 - - + -
75G LYS 4.7 3.1 + - - +
76G ASN* 3.2 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G GLN 4.3 1.4 - - - +
2G VAL* 3.6 8.0 - - - +
3G GLN* 3.3 36.0 + - - -
24G ALA* 1.3 80.1 - - - +
26G GLY* 1.3 63.9 + - - +
27G ARG 3.4 4.5 + - - +
29G PHE* 5.1 0.2 - - - -
76G ASN* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il